The beginning of his reign was marked by the Danish defeat in the Second Schleswig War and the subsequent loss of the duchies of Schleswig, Holstein and Lauenburg which made the king immensely unpopular. The following years of his reign were dominated by political disputes as Denmark had only become a constitutional monarchy in 1849 and the balance of power between the sovereign and parliament was still in dispute. In spite of his initial unpopularity and the many years of political strife, where the king was in conflict with large parts of the population, his popularity recovered towards the end of his reign, and he became a national icon due to the length of his reign and the high standards of personal morality with which he was identified.

Frederick VII's childlessness had presented a thorny dilemma and the question of succession to the Danish throne proved problematic. Denmark's adherence to the Salic Law and a burgeoning nationalism within the German-speaking parts of Schleswig-Holstein hindered all hopes of a peaceful solution. Proposed resolutions to keep the two Duchies together and part of Denmark proved unsatisfactory to both Danish and German interests. While Denmark had adopted the Salic Law, this only affected the descendants of Frederick III of Denmark, who was the first hereditary monarch of Denmark (before him, the kingdom was officially elective). Agnatic descent from Frederick III would end with the death of the childless King Frederick VII and his equally childless uncle, Prince Ferdinand. At that point, the law of succession promulgated by Frederick III provided for a Semi-Salic succession. There were, however, several ways to interpret to whom the crown could pass, since the provision was not entirely clear as to whether a claimant to the throne could be the closest female relative or not.

The dynastic female heiress reckoned most eligible according to the original law of primogeniture of Frederick III was Caroline of Denmark (1793–1881), the childless eldest daughter of the late king Frederick VI. Along with another childless daughter, Wilhelmine of Denmark (1808–1891), Duchess of Glücksburg; the next heir was Louise, sister of Frederick VI, who had married the Duke of Augustenburg. The chief heir to that line was the selfsame Frederick of Augustenburg, but his turn would have come only after the death of two childless princesses who were very much alive in 1863.

The House of Glücksburg also held a significant interest in the succession to the throne. A more junior branch of the royal clan, they were also descendants of Frederick III through the daughter of King Frederick V of Denmark. Lastly, there was yet a more junior agnatic branch that was eligible to succeed in Schleswig-Holstein. There was Christian himself and his three older brothers, the eldest of whom, Karl, was childless, but the others had produced children, and male children at that.

Prince Christian had been a foster "grandson" of the "grandchildless" royal couple Frederick VI and his Queen consort Marie (Marie Sophie Friederike of Hesse). Familiar with the royal court and the traditions of the recent monarchs, their young ward Prince Christian was great-nephew of Queen Marie and descendant of a first cousin of Frederick VI. He was brought up as Danish, having lived in Danish-speaking lands of the royal dynasty and had not become a German nationalist, which made him a relatively good candidate from the Danish point of view. As junior agnatic descendant, he was eligible to inherit Schleswig-Holstein, but was not the first in line. As a descendant of Frederick III, he was eligible to succeed in Denmark, although here too, he was not first-in-line.

In 1842, Christian married Princess Louise of Hesse, daughter of the closest female relative of Frederick VII. Louise's mother and brother, and elder sister too, renounced their rights in favor of Louise and her husband. Prince Christian's wife was now the closest female heiress of Frederick VII.

In 1852, the thorny question of Denmark's succession was resolved by the London Protocol of 8 May 1852, through which Christian was chosen as next-in-line for the throne after Frederick VII and his uncle. The decision was implemented by the Danish Law of Succession of 31 July 1853—more precisely, the Royal Ordinance settling the Succession to the Crown on Prince Christian of Glücksburg[1]—which designated him as heir to the entire Danish monarchy following the extinction of the male line of Frederick III and granted him the titlePrince of Denmark.

Upon the death of Frederick VII on 15 November 1863, Christian succeeded to the throne as Christian IX. Denmark was immediately plunged into a crisis over the possession and status of Schleswig and Holstein, two provinces to Denmark's south. In November 1863 Frederick of Augustenburg claimed the twin-duchies in succession after King Frederick. Under pressure, Christian signed the November Constitution, a treaty that made Schleswig part of Denmark. This resulted in the Second Schleswig War between Denmark and a Prussian/Austrian alliance in 1864. The Peace Conference broke up without having arrived at any conclusion; the outcome of the war was unfavorable to Denmark and led to the incorporation of Schleswig into Prussia in 1865. Holstein was likewise incorporated into in 1865, following further conflict between Austria and Prussia.

Following the loss, Christian IX went behind the backs of the Danish government to contact the Prussians, offering that the whole of Denmark could join the German confederation, if Denmark could stay united with Schleswig and Holstein. This proposal was rejected by Bismarck, who feared that the ethnic strife in Schleswig between Danes and Germans would then stay unresolved. Christian IX's negotiations were not publicly known until published in the 2010 book Dommedag Als by Tom Buk-Swientys, who had been given access to the royal archives by Queen Margrethe II.[2]

The defeat of 1864 cast a shadow over Christian IX's rule for many years and his attitude to the Danish case—probably without reason—was claimed to be half-hearted. This unpopularity was worsened as he sought unsuccessfully to prevent the spread of democracy throughout Denmark by supporting the authoritarian and conservative prime minister Estrup, whose rule 1875–94 was by many seen as a semi-dictatorship. However, he signed a treaty in 1874 which allowed Iceland, then a Danish possession, to have its own constitution, albeit one that still had Denmark ruling Iceland. In 1901, he reluctantly asked Johan Henrik Deuntzer to form a government and this resulted in the formation of the Cabinet of Deuntzer. The cabinet consisted of members of the Venstre Reform Party and was the first Danish government not to include the conservative party Højre, even though Højre never had a majority of the seats in the Folketing. This was the beginning of the Danish tradition of parliamentarism and clearly bettered his reputation for his last years.

Another reform occurred in 1866, when the Danish constitution was revised so that Denmark's upper chamber would have more power than the lower. Social security also took a few steps forward during his reign. Old age pensions were introduced in 1891 and unemployment and family benefits were introduced in 1892.

Christian's family links with Europe's royal families earned him the sobriquet "the father-in-law of Europe". Four of Christian's children sat on the thrones (either as monarchs or as consorts) of Denmark, the United Kingdom, Russia, and Greece. His daughter Thyra would have become Queen of Hanover had her husband's throne not been abolished before his reign began.[citation needed] His youngest son, Valdemar, was offered the crowns of Bulgaria and Norway, but had to decline both under international pressure[citation needed], but his grandson Charles later accepted the crown of Norway.

The great dynastic success of the six children was to a great extent not attributable to Christian himself, but the result of the ambitions of his wife Louise of Hesse-Kassel. Some have compared her dynastical capabilities to those of Queen Victoria of the United Kingdom.[citation needed] An additional factor was that Denmark was not one of the Great Powers, so the other powers did not fear that the balance of power in Europe would be upset by a marriage of one of its royalty to another royal house.